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<title>shiny4RefPlantNLR</title>

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<h1 class="title toc-ignore">shiny4RefPlantNLR</h1>



<div class="sourceCode" id="cb1"><pre class="sourceCode r"><code class="sourceCode r"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(shiny4RefPlantNLR)</span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：shinydashboard</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: 程辑包&#39;shinydashboard&#39;是用R版本4.1.1 来建造的</span></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入程辑包：&#39;shinydashboard&#39;</span></span>
<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; The following object is masked from &#39;package:graphics&#39;:</span></span>
<span id="cb1-7"><a href="#cb1-7" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-8"><a href="#cb1-8" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     box</span></span>
<span id="cb1-9"><a href="#cb1-9" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：shiny</span></span>
<span id="cb1-10"><a href="#cb1-10" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: 程辑包&#39;shiny&#39;是用R版本4.1.1 来建造的</span></span>
<span id="cb1-11"><a href="#cb1-11" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：thinkr</span></span>
<span id="cb1-12"><a href="#cb1-12" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: 程辑包&#39;thinkr&#39;是用R版本4.1.1 来建造的</span></span>
<span id="cb1-13"><a href="#cb1-13" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：shinyWidgets</span></span>
<span id="cb1-14"><a href="#cb1-14" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: 程辑包&#39;shinyWidgets&#39;是用R版本4.1.1 来建造的</span></span>
<span id="cb1-15"><a href="#cb1-15" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：dplyr</span></span>
<span id="cb1-16"><a href="#cb1-16" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-17"><a href="#cb1-17" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入程辑包：&#39;dplyr&#39;</span></span>
<span id="cb1-18"><a href="#cb1-18" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; The following objects are masked from &#39;package:stats&#39;:</span></span>
<span id="cb1-19"><a href="#cb1-19" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-20"><a href="#cb1-20" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     filter, lag</span></span>
<span id="cb1-21"><a href="#cb1-21" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; The following objects are masked from &#39;package:base&#39;:</span></span>
<span id="cb1-22"><a href="#cb1-22" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-23"><a href="#cb1-23" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     intersect, setdiff, setequal, union</span></span>
<span id="cb1-24"><a href="#cb1-24" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：data.table</span></span>
<span id="cb1-25"><a href="#cb1-25" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: 程辑包&#39;data.table&#39;是用R版本4.1.1 来建造的</span></span>
<span id="cb1-26"><a href="#cb1-26" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-27"><a href="#cb1-27" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入程辑包：&#39;data.table&#39;</span></span>
<span id="cb1-28"><a href="#cb1-28" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; The following objects are masked from &#39;package:dplyr&#39;:</span></span>
<span id="cb1-29"><a href="#cb1-29" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-30"><a href="#cb1-30" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     between, first, last</span></span>
<span id="cb1-31"><a href="#cb1-31" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：stringr</span></span>
<span id="cb1-32"><a href="#cb1-32" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：markdown</span></span>
<span id="cb1-33"><a href="#cb1-33" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：knitr</span></span>
<span id="cb1-34"><a href="#cb1-34" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: 程辑包&#39;knitr&#39;是用R版本4.1.1 来建造的</span></span>
<span id="cb1-35"><a href="#cb1-35" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：reshape2</span></span>
<span id="cb1-36"><a href="#cb1-36" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-37"><a href="#cb1-37" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入程辑包：&#39;reshape2&#39;</span></span>
<span id="cb1-38"><a href="#cb1-38" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; The following objects are masked from &#39;package:data.table&#39;:</span></span>
<span id="cb1-39"><a href="#cb1-39" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-40"><a href="#cb1-40" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;     dcast, melt</span></span>
<span id="cb1-41"><a href="#cb1-41" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：ggmsa</span></span>
<span id="cb1-42"><a href="#cb1-42" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: 程辑包&#39;ggmsa&#39;是用R版本4.1.1 来建造的</span></span>
<span id="cb1-43"><a href="#cb1-43" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Registered S3 methods overwritten by &#39;ggalt&#39;:</span></span>
<span id="cb1-44"><a href="#cb1-44" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   method                  from   </span></span>
<span id="cb1-45"><a href="#cb1-45" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   grid.draw.absoluteGrob  ggplot2</span></span>
<span id="cb1-46"><a href="#cb1-46" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   grobHeight.absoluteGrob ggplot2</span></span>
<span id="cb1-47"><a href="#cb1-47" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   grobWidth.absoluteGrob  ggplot2</span></span>
<span id="cb1-48"><a href="#cb1-48" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   grobX.absoluteGrob      ggplot2</span></span>
<span id="cb1-49"><a href="#cb1-49" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt;   grobY.absoluteGrob      ggplot2</span></span>
<span id="cb1-50"><a href="#cb1-50" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ggmsa v1.0.0  Document: http://yulab-smu.top/ggmsa/</span></span>
<span id="cb1-51"><a href="#cb1-51" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-52"><a href="#cb1-52" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; If you use ggmsa in published research, please cite: DOI: 10.18129/B9.bioc.ggmsa</span></span>
<span id="cb1-53"><a href="#cb1-53" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：ggtree</span></span>
<span id="cb1-54"><a href="#cb1-54" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: 程辑包&#39;ggtree&#39;是用R版本4.1.1 来建造的</span></span>
<span id="cb1-55"><a href="#cb1-55" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; ggtree v3.2.0  For help: https://yulab-smu.top/treedata-book/</span></span>
<span id="cb1-56"><a href="#cb1-56" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-57"><a href="#cb1-57" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; If you use ggtree in published research, please cite the most appropriate paper(s):</span></span>
<span id="cb1-58"><a href="#cb1-58" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-59"><a href="#cb1-59" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 1. Guangchuang Yu. Using ggtree to visualize data on tree-like structures. Current Protocols in Bioinformatics. 2020, 69:e96. doi:10.1002/cpbi.96</span></span>
<span id="cb1-60"><a href="#cb1-60" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 2. Guangchuang Yu, Tommy Tsan-Yuk Lam, Huachen Zhu, Yi Guan. Two methods for mapping and visualizing associated data on phylogeny using ggtree. Molecular Biology and Evolution. 2018, 35(12):3041-3043. doi:10.1093/molbev/msy194</span></span>
<span id="cb1-61"><a href="#cb1-61" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 3. Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution. 2017, 8(1):28-36. doi:10.1111/2041-210X.12628</span></span>
<span id="cb1-62"><a href="#cb1-62" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; 载入需要的程辑包：treeio</span></span>
<span id="cb1-63"><a href="#cb1-63" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; Warning: 程辑包&#39;treeio&#39;是用R版本4.1.1 来建造的</span></span>
<span id="cb1-64"><a href="#cb1-64" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; treeio v1.18.0  For help: https://yulab-smu.top/treedata-book/</span></span>
<span id="cb1-65"><a href="#cb1-65" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-66"><a href="#cb1-66" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; If you use treeio in published research, please cite:</span></span>
<span id="cb1-67"><a href="#cb1-67" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; </span></span>
<span id="cb1-68"><a href="#cb1-68" aria-hidden="true" tabindex="-1"></a><span class="co">#&gt; LG Wang, TTY Lam, S Xu, Z Dai, L Zhou, T Feng, P Guo, CW Dunn, BR Jones, T Bradley, H Zhu, Y Guan, Y Jiang, G Yu. treeio: an R package for phylogenetic tree input and output with richly annotated and associated data. Molecular Biology and Evolution 2020, 37(2):599-603. doi: 10.1093/molbev/msz240</span></span></code></pre></div>



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